Hierarchical Catalogue Generation for Literature Review: A Benchmark

Multi-document scientific summarization can extract and organize important information from an abundant collection of papers, arousing widespread attention recently. However, existing efforts focus on producing lengthy overviews lacking a clear and logical hierarchy. To alleviate this problem, we present an atomic and challenging task named Hierarchical Catalogue Generation for Literature Review (HiCatGLR), which aims to generate a hierarchical catalogue for a review paper given various references. We carefully construct a novel English Hierarchical Catalogues of Literature Reviews Dataset (HiCaD) with 13.8k literature review catalogues and 120k reference papers, where we benchmark diverse experiments via the end-to-end and pipeline methods. To accurately assess the model performance, we design evaluation metrics for similarity to ground truth from semantics and structure. Besides, our extensive analyses verify the high quality of our dataset and the effectiveness of our evaluation metrics. Furthermore, we discuss potential directions for this task to motivate future research

'Don't Get Too Technical with Me': A Discourse Structure-Based Framework for Science Journalism

Science journalism refers to the task of reporting technical findings of a scientific paper as a less technical news article to the general public audience. We aim to design an automated system to support this real-world task (i.e., automatic science journalism) by 1) introducing a newly-constructed and real-world dataset (SciTechNews), with tuples of a publicly-available scientific paper, its corresponding news article, and an expert-written short summary snippet; 2) proposing a novel technical framework that integrates a paper's discourse structure with its metadata to guide generation; and, 3) demonstrating with extensive automatic and human experiments that our framework outperforms other baseline methods (e.g. Alpaca and ChatGPT) in elaborating a content plan meaningful for the target audience, simplifying the information selected, and producing a coherent final report in a layman's style.Comment: Accepted to EMNLP 202

Literature Retrieval for Precision Medicine with Neural Matching and Faceted Summarization

Information retrieval (IR) for precision medicine (PM) often involves looking for multiple pieces of evidence that characterize a patient case. This typically includes at least the name of a condition and a genetic variation that applies to the patient. Other factors such as demographic attributes, comorbidities, and social determinants may also be pertinent. As such, the retrieval problem is often formulated as ad hoc search but with multiple facets (e.g., disease, mutation) that may need to be incorporated. In this paper, we present a document reranking approach that combines neural query-document matching and text summarization toward such retrieval scenarios. Our architecture builds on the basic BERT model with three specific components for reranking: (a). document-query matching (b). keyword extraction and (c). facet-conditioned abstractive summarization. The outcomes of (b) and (c) are used to essentially transform a candidate document into a concise summary that can be compared with the query at hand to compute a relevance score. Component (a) directly generates a matching score of a candidate document for a query. The full architecture benefits from the complementary potential of document-query matching and the novel document transformation approach based on summarization along PM facets. Evaluations using NIST's TREC-PM track datasets (2017--2019) show that our model achieves state-of-the-art performance. To foster reproducibility, our code is made available here: https://github.com/bionlproc/text-summ-for-doc-retrieval.Comment: Accepted to EMNLP 2020 Findings as Long Paper (11 page, 4 figures

Literature Retrieval for Precision Medicine with Neural Matching and Faceted Summarization

Information retrieval (IR) for precision medicine (PM) often involves looking for multiple pieces of evidence that characterize a patient case. This typically includes at least the name of a condition and a genetic variation that applies to the patient. Other factors such as demographic attributes, comorbidities, and social determinants may also be pertinent. As such, the retrieval problem is often formulated as ad hoc search but with multiple facets (e.g., disease, mutation) that may need to be incorporated. In this paper, we present a document reranking approach that combines neural query-document matching and text summarization toward such retrieval scenarios. Our architecture builds on the basic BERT model with three specific components for reranking: (a). document-query matching (b). keyword extraction and (c). facet-conditioned abstractive summarization. The outcomes of (b) and (c) are used to essentially transform a candidate document into a concise summary that can be compared with the query at hand to compute a relevance score. Component (a) directly generates a matching score of a candidate document for a query. The full architecture benefits from the complementary potential of document-query matching and the novel document transformation approach based on summarization along PM facets. Evaluations using NIST’s TREC-PM track datasets (2017–2019) show that our model achieves state-of-the-art performance. To foster reproducibility, our code is made available here: https://github.com/bionlproc/text-summ-for-doc-retrieval

State-of-the-art generalisation research in NLP: a taxonomy and review

The ability to generalise well is one of the primary desiderata of natural language processing (NLP). Yet, what `good generalisation' entails and how it should be evaluated is not well understood, nor are there any common standards to evaluate it. In this paper, we aim to lay the ground-work to improve both of these issues. We present a taxonomy for characterising and understanding generalisation research in NLP, we use that taxonomy to present a comprehensive map of published generalisation studies, and we make recommendations for which areas might deserve attention in the future. Our taxonomy is based on an extensive literature review of generalisation research, and contains five axes along which studies can differ: their main motivation, the type of generalisation they aim to solve, the type of data shift they consider, the source by which this data shift is obtained, and the locus of the shift within the modelling pipeline. We use our taxonomy to classify over 400 previous papers that test generalisation, for a total of more than 600 individual experiments. Considering the results of this review, we present an in-depth analysis of the current state of generalisation research in NLP, and make recommendations for the future. Along with this paper, we release a webpage where the results of our review can be dynamically explored, and which we intend to up-date as new NLP generalisation studies are published. With this work, we aim to make steps towards making state-of-the-art generalisation testing the new status quo in NLP.Comment: 35 pages of content + 53 pages of reference

Bringing order into the realm of Transformer-based language models for artificial intelligence and law

Transformer-based language models (TLMs) have widely been recognized to be a cutting-edge technology for the successful development of deep-learning-based solutions to problems and applications that require natural language processing and understanding. Like for other textual domains, TLMs have indeed pushed the state-of-the-art of AI approaches for many tasks of interest in the legal domain. Despite the first Transformer model being proposed about six years ago, there has been a rapid progress of this technology at an unprecedented rate, whereby BERT and related models represent a major reference, also in the legal domain. This article provides the first systematic overview of TLM-based methods for AI-driven problems and tasks in the legal sphere. A major goal is to highlight research advances in this field so as to understand, on the one hand, how the Transformers have contributed to the success of AI in supporting legal processes, and on the other hand, what are the current limitations and opportunities for further research development.Comment: Please refer to the published version: Greco, C.M., Tagarelli, A. (2023) Bringing order into the realm of Transformer-based language models for artificial intelligence and law. Artif Intell Law, Springer Nature. November 2023. https://doi.org/10.1007/s10506-023-09374-

Language modelling for clinical natural language understanding and generation

One of the long-standing objectives of Artificial Intelligence (AI) is to design and develop algorithms for social good including tackling public health challenges. In the era of digitisation, with an unprecedented amount of healthcare data being captured in digital form, the analysis of the healthcare data at scale can lead to better research of diseases, better monitoring patient conditions and more importantly improving patient outcomes. However, many AI-based analytic algorithms rely solely on structured healthcare data such as bedside measurements and test results which only account for 20% of all healthcare data, whereas the remaining 80% of healthcare data is unstructured including textual data such as clinical notes and discharge summaries which is still underexplored. Conventional Natural Language Processing (NLP) algorithms that are designed for clinical applications rely on the shallow matching, templates and non-contextualised word embeddings which lead to limited understanding of contextual semantics. Though recent advances in NLP algorithms have demonstrated promising performance on a variety of NLP tasks in the general domain with contextualised language models, most of these generic NLP algorithms struggle at specific clinical NLP tasks which require biomedical knowledge and reasoning. Besides, there is limited research to study generative NLP algorithms to generate clinical reports and summaries automatically by considering salient clinical information. This thesis aims to design and develop novel NLP algorithms especially clinical-driven contextualised language models to understand textual healthcare data and generate clinical narratives which can potentially support clinicians, medical scientists and patients. The first contribution of this thesis focuses on capturing phenotypic information of patients from clinical notes which is important to profile patient situation and improve patient outcomes. The thesis proposes a novel self-supervised language model, named Phenotypic Intelligence Extraction (PIE), to annotate phenotypes from clinical notes with the detection of contextual synonyms and the enhancement to reason with numerical values. The second contribution is to demonstrate the utility and benefits of using phenotypic features of patients in clinical use cases by predicting patient outcomes in Intensive Care Units (ICU) and identifying patients at risk of specific diseases with better accuracy and model interpretability. The third contribution is to propose generative models to generate clinical narratives to automate and accelerate the process of report writing and summarisation by clinicians. This thesis first proposes a novel summarisation language model named PEGASUS which surpasses or is on par with the state-of-the-art performance on 12 downstream datasets including biomedical literature from PubMed. PEGASUS is further extended to generate medical scientific documents from input tabular data.Open Acces